The most usual culprit is the filling being a bit too soft - it can't take the weight of the cake/paste on top. I take it the top tier is being supported and isn't just sitting on the base? If not, that will def be adding to the problem.

I haven't found a way to fix it I'm afraid, but maybe some bright spark will have a secret weapon up their sleeve :)

You'll get different answers on this. However, when you have a softer filling, it will compress just a little. One way to reduce this effect is to compress your cake after you fill it and before you cover it with fondant. Some simply push it down by hand. Some people put a large ceramic tile on the filled cake for a few hours or overnight. The idea is to get these bulges to show up before you cover the cake in fondant.

Some will say this is unnecessary. They may be using a stiffer filling. The need for this depends on your filling consistency.

AUse a stiffer frosting to dam the cake, fill with any type of filling. I got a tip from a fellow bake that her dam consisted of frosting and a bit of cake crumbs so that it's so thick the you can almost roll your buttercream.

Yes, let the cake settle. If this is for a bottom tier or if you have a cake topper on top, you can dowel the cake and take the dowel out. Yes, the cake is already covered in fondant at this stage. This will give the cake a hole where trapped air can escape. This was also a tip given by a fellow caker. It works wonder for me :)
Goodluck!

When I have a cake to do with a soft filling, I ALWAYS pipe a border along the edge of each layer of cake and then you can place your softer filling in the middle to smooth out before stacking. The icing used for the border needs to be very stiff. I use a very stiff butter cream recipe that is relatively firm even at room temp. This way even if the cake is out of the fridge, this border should hold in the soft icing center. I have used whipped cream, custards etc. for the filling with no problems with bulging at all afterwords. Hope this helps!